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- PDB-5y88: Cryo-EM structure of the intron-lariat spliceosome ready for disa... -

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Entry
Database: PDB / ID: 5y88
TitleCryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom
Components
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 16
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • Intron lariat
  • Pre-mRNA-processing protein 45
  • Protein CWC16
  • RNA (intron or U6 snRNA)
  • Small nuclear ribonucleoprotein-associated protein B
  • U2 snRNAU2 spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
KeywordsSPLICING / ILS complex / Ntr complex / disassembly / Prp43
Function / homologyRNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein Sm D2 / P-loop containing nucleoside triphosphate hydrolase / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor Ntr2 / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Torus domain / Leucine-rich repeat domain superfamily ...RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein Sm D2 / P-loop containing nucleoside triphosphate hydrolase / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor Ntr2 / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Torus domain / Leucine-rich repeat domain superfamily / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein D1 / PRP8 domain IV core / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Slt11-like, RNA recognition motif / EF-G domain III/V-like / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / RNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Chaperone J-domain superfamily / MPN domain / Pre-mRNA-processing factor 19 / Pre-mRNA-splicing factor Cwc2/Slt11 / Pre-mRNA-splicing factor Cwc2 / Small nuclear ribonucleoprotein E / Pre-mRNA splicing factor component Cdc5p/Cef1 / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein S5 domain 2-type fold, subgroup / Tetratricopeptide-like helical domain superfamily / Ribonuclease H-like superfamily / PRO8NT domain / PROCN domain / Nucleotide-binding alpha-beta plait domain superfamily / PROCT domain / Tetratricopeptide repeat-containing domain / Zinc finger, RING/FYVE/PHD-type / mRNA splicing factor SYF2 / Pre-mRNA-splicing factor 19 / Helicase superfamily 1/2, ATP-binding domain / Myb-like transcription factor / Ribosomal protein S5 domain 2-type fold / Sm-like protein Lsm6/SmF / SKI-interacting protein, SKIP / Myb domain / WD40-repeat-containing domain / BUD31/G10-related, conserved site / DnaJ domain, conserved site / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Elongation factor Tu GTP binding domain / DnaJ domain / DEAD/DEAH box helicase domain / Trp-Asp (WD) repeats circular profile. / Nt-dnaJ domain signature. / Trp-Asp (WD) repeats signature. / DEAH-box subfamily ATP-dependent helicases signature. / G10 protein signature 1. / G10 protein signature 2. / dnaJ domain profile. / Trp-Asp (WD) repeats profile. / Eukaryotic RNA Recognition Motif (RRM) profile. / Zinc finger C3H1-type profile. / G-patch domain profile. / MPN domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Superfamilies 1 and 2 helicase C-terminal domain profile. / Myb-type HTH DNA-binding domain profile. / Leucine-rich repeat profile. / U-box domain profile. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / mRNA decay by 5' to 3' exoribonuclease / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Minor Pathway / Leucine-rich repeat / Torus domain / Nineteen complex-related protein 2 / Myb-like DNA-binding domain / Helicase associated domain (HA2) / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / WD domain, G-beta repeat / Elongation factor G C-terminus / G10 protein / LSM domain / G-patch domain / HAT (Half-A-TPR) repeat / SKIP/SNW domain / Elongation factor Tu domain 2 / Elongation factor G, domain IV / Family of unknown function (DUF572) / PRP8 domain IV core / Cwf15/Cwc15 cell cycle control protein
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.46 Å resolution
AuthorsWan, R. / Yan, C. / Bai, R. / Lei, J. / Shi, Y.
CitationJournal: Cell / Year: 2017
Title: Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae.
Authors: Ruixue Wan / Chuangye Yan / Rui Bai / Jianlin Lei / Yigong Shi
Abstract: The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an ...The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an average resolution of 3.5 Å. The intron lariat remains bound in the spliceosome whereas the ligated exon is already dissociated. The step II splicing factors Prp17 and Prp18, along with Cwc21 and Cwc22 that stabilize the 5' exon binding to loop I of U5 small nuclear RNA (snRNA), have been released from the active site assembly. The DEAH family ATPase/helicase Prp43 binds Syf1 at the periphery of the spliceosome, with its RNA-binding site close to the 3' end of U6 snRNA. The C-terminal domain of Ntr1/Spp382 associates with the GTPase Snu114, and Ntr2 is anchored to Prp8 while interacting with the superhelical domain of Ntr1. These structural features suggest a plausible mechanism for the disassembly of the ILS complex.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 20, 2017 / Release: Aug 1, 2018

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Structure visualization

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor 8
B: U5 snRNA
C: Pre-mRNA-splicing factor SNU114
D: U6 snRNA
E: Intron lariat
F: U2 snRNA
G: Pre-mRNA-splicing factor SNT309
H: Pre-mRNA-splicing factor SYF1
I: Pre-mRNA-splicing factor CLF1
J: Pre-mRNA-splicing factor CEF1
K: Pre-mRNA-splicing factor SYF2
L: Pre-mRNA-splicing factor BUD31
M: Pre-mRNA-splicing factor SLT11
N: Pre-mRNA-splicing factor CWC2
O: Pre-mRNA-splicing factor PRP46
P: Pre-mRNA-splicing factor CWC15
Q: Pre-mRNA-processing protein 45
R: Protein CWC16
S: Pre-mRNA-processing factor 17
T: Pre-mRNA-splicing factor CWC23
U: Pre-mRNA-splicing factor SPP382
V: Pre-mRNA-splicing factor NTR2
W: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
a: Small nuclear ribonucleoprotein-associated protein B
b: Small nuclear ribonucleoprotein E
c: Small nuclear ribonucleoprotein F
d: Small nuclear ribonucleoprotein G
e: Small nuclear ribonucleoprotein Sm D3
f: Small nuclear ribonucleoprotein Sm D1
g: Small nuclear ribonucleoprotein Sm D2
o: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
h: Small nuclear ribonucleoprotein-associated protein B
i: Small nuclear ribonucleoprotein E
j: Small nuclear ribonucleoprotein F
k: Small nuclear ribonucleoprotein G
l: Small nuclear ribonucleoprotein Sm D3
m: Small nuclear ribonucleoprotein Sm D1
n: Small nuclear ribonucleoprotein Sm D2
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
x: RNA (intron or U6 snRNA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,172,36058
Polyers2,170,63944
Non-polymers1,72114
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Pre-mRNA-splicing factor ... , 16 types, 16 molecules ACGHIJKLMNOPTUVW

#1: Protein/peptide Pre-mRNA-splicing factor 8


Mass: 279867.469 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33334
#3: Protein/peptide Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10


Mass: 114174.008 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36048
#7: Protein/peptide Pre-mRNA-splicing factor SNT309 / PRP19-associated complex protein 25 / Synergistic to PRP19 mutation protein 309


Mass: 20741.455 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06091
#8: Protein/peptide Pre-mRNA-splicing factor SYF1 / PRP19-associated complex protein 90 / Synthetic lethal with CDC40 protein 1


Mass: 100344.016 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04048
#9: Protein/peptide Pre-mRNA-splicing factor CLF1 / Crooked neck-like factor 1 / PRP19-associated complex protein 77 / Synthetic lethal with CDC40 protein 3


Mass: 82555.859 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12309
#10: Protein/peptide Pre-mRNA-splicing factor CEF1 / PRP nineteen-associated complex protein 85 / PRP19-associated complex protein 85


Mass: 67837.773 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03654
#11: Protein/peptide Pre-mRNA-splicing factor SYF2 / PRP19 complex protein 31 / Synthetic lethal with CDC40 protein 2


Mass: 24850.719 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53277
#12: Protein/peptide Pre-mRNA-splicing factor BUD31 / Bud site selection protein 31 / Complexed with CEF1 protein 14


Mass: 18484.502 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25337
#13: Protein/peptide Pre-mRNA-splicing factor SLT11 / Extracellular mutant protein 2 / Synthetic lethality with U2 protein 11


Mass: 40988.590 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38241
#14: Protein/peptide Pre-mRNA-splicing factor CWC2 / Complexed with CEF1 protein 2 / PRP19-associated complex protein 40 / Synthetic lethal with CLF1 protein 3


Mass: 38486.562 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12046
#15: Protein/peptide Pre-mRNA-splicing factor PRP46 / Complexed with CEF1 protein 1 / PRP nineteen-associated complex protein 50 / PRP19-associated complex protein 50 / Pre-mRNA-processing protein 46


Mass: 50771.289 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12417
#16: Protein/peptide Pre-mRNA-splicing factor CWC15 / Complexed with CEF1 protein 15


Mass: 19975.195 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03772
#20: Protein/peptide Pre-mRNA-splicing factor CWC23 / Complexed with CEF1 protein 23


Mass: 33280.355 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P52868
#21: Protein/peptide Pre-mRNA-splicing factor SPP382 / CLF1 complex factor 8 / Nineteen complex-related protein 1 / NTC-related protein 1 / Suppressor of PRP38 protein 2


Mass: 83155.453 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06411
#22: Protein/peptide Pre-mRNA-splicing factor NTR2 / Nineteen complex-related protein 2 / NTC-related protein 2


Mass: 36705.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36118
#23: Protein/peptide Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 / Helicase JA1


Mass: 87682.750 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53131, RNA helicase

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RNA chain , 5 types, 5 molecules BDEFx

#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 68643.344 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
#4: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 35883.176 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 1039023367
#5: RNA chain Intron lariat


Mass: 10810.159 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
#6: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 376267.406 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
#34: RNA chain RNA (intron or U6 snRNA)


Mass: 2710.535 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c

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Protein/peptide , 3 types, 4 molecules QRah

#17: Protein/peptide Pre-mRNA-processing protein 45


Mass: 42548.727 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P28004
#18: Protein/peptide Protein CWC16


Mass: 32371.086 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P28320
#24: Protein/peptide Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB


Mass: 22426.990 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40018

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Pre-mRNA-processing factor ... , 2 types, 5 molecules Sqrst

#19: Protein/peptide Pre-mRNA-processing factor 17 / Cell division control protein 40


Mass: 52128.762 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40968
#33: Protein/peptide
Pre-mRNA-processing factor 19 / RING-type E3 ubiquitin transferase PRP19


Mass: 56629.777 Da / Num. of mol.: 4
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32523, EC: 2.3.2.27

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules bicjdkelfmgn

#25: Protein/peptide Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10385.098 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12330
#26: Protein/peptide Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P54999
#27: Protein/peptide Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40204
#28: Protein/peptide Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 11240.139 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P43321
#29: Protein/peptide Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 16296.798 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02260
#30: Protein/peptide Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 12876.066 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06217

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#31: Protein/peptide U2 small nuclear ribonucleoprotein A' / U2 snRNP A' / Looks exceptionally like U2A protein 1


Mass: 27232.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08963
#32: Protein/peptide U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 12850.944 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40567

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Non-polymers , 4 types, 14 molecules

#35: Chemical ChemComp-I6P / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Formula: C6H18O24P6 / Phytic acid
#36: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#37: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Formula: Mg / Magnesium
#38: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Formula: Zn / Zinc

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Details

Sequence detailsThe author doesn't know the sequence between 16-491 of chain E.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: S. cerevisiae intron lariat spliceosome (ILS) / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: S288c
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 37.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
EM software
IDNameVersionCategory
2UCSFImage4image acquisition
4GctfCTF correction
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
12RELION2.0classification
13RELION2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 150363 / Symmetry type: POINT
Least-squares processHighest resolution: 3.7 Å
Number of atoms included #1Total: 41773
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.01843207
ELECTRON MICROSCOPYr_bond_other_d0.0020.02038093
ELECTRON MICROSCOPYr_angle_refined_deg1.4561.84959683
ELECTRON MICROSCOPYr_angle_other_deg0.9603.00088056
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.6665.0004407
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.38723.9271724
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.64715.0006713
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.75815.000261
ELECTRON MICROSCOPYr_chiral_restr0.0820.2006529
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.02144061
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0209859
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it9.06712.60217754
ELECTRON MICROSCOPYr_mcbond_other9.06712.60117753
ELECTRON MICROSCOPYr_mcangle_it14.99118.89522119
ELECTRON MICROSCOPYr_mcangle_other14.99118.89622120
ELECTRON MICROSCOPYr_scbond_it9.81813.98025453
ELECTRON MICROSCOPYr_scbond_other9.81813.98125454
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other16.57920.68337565
ELECTRON MICROSCOPYr_long_range_B_refined28.378176928
ELECTRON MICROSCOPYr_long_range_B_other28.378176929
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.7 Å / R factor R work: 0.391 / Lowest resolution: 3.796 Å / Number reflection R free: 0 / Number reflection R work: 20983 / Total number of bins used: 20 / Percent reflection obs: 1

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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